1.1 ක්ෂුද්‍රජීවීන්ගේ� ස්වා�භා�වාය හා� විවිධත්වාය: ඒකකය

1

I.ක්ෂුද්‍රජීවා විද්‍යා��වා හා�ද්‍යා�රීගේ� වා�ද්‍යාගත්කම

1. මා�නව සෞ��ඛ්‍යයට වන බලපෑ�මා - සෞ��ගකා��කා වෛව�ස්, බ�ක්ටීරිය�, සෞපෑ��සෞට�සෞ��ව�වන්

2. පෑරි�� �මාතුලිතත�වය - ආහා�� පෑ�භවයක් , විසෞය�ජකායන් සෞල� පෑ�ධා�න සෞමාසෞහායක්

ඉටු කාරීමා, ඇත�ම් �තුන්ට ආහා�� ජීර්ණය �දහා� ආධා�� වීමා (බ�ටළුවන්, ගවයන්,

සෞ1යන් ව�නි �තුන්සෞ3 ආහා�� මා�ර්ග වල)

3.   පෑරි��යට හිතකා� නිෂ්පෑ�දන - වෛජව හා�යනයට ලක් වන ද්‍රව නිපෑදවීමා, සු�ක්ෂිත

පෑ�නීය ජලය, සෞතල් කා�න්දුවීම්- බ�ක්ටීරිය� භ�විතසෞයන් ඉවත් කිරීමා -

bioremediation.

4.  කා�ර්මිකා නිෂ්පෑ�දන– ආහා�� වර්ග (පෑ�න්, චීස්, බියර්, වයින්, සෞවනත් ආහා��), පෑ�තිසෞCහා,

ඉන්සියුලින්, වෛජව ඉFජිසෞන්�� ත�ක්ෂණය)

5. කාIෂිකා�ර්මිකා - සෞ��ඛ්‍යයට හිතකා� මා�Fෂ වර්ග �හා සෞ��ග වලින් සෞත�� සෞභ�ග වර්ග

නිෂ්පෑ�දනය

�දහා� නි�න්ත� පෑරීක්ෂණ සිදු සෞකාසෞර්.

 II. ක්ෂුද්‍රජීවා විද්‍යා��වා

ක්ෂුද්‍රජීවා විද්‍යා��වා යනු පියවි ඇ�ට සෞන�සෞපෑසෞනන (0.1 mm ට වඩා� කුඩා�) ක්ෂුද්‍රජීවීන් පිළිබද

අධායනයි.

ක්ෂුද්‍රජීවා විද්‍යා��ගේ� ඉතිහා�සය Leeuwenhoeck (lived 1632-1723) –

අන්වීක්ෂය “animalcules.” - ක්ෂුද්‍රජීවීන්

Hooke (1665) “cellulae” - සෛසලය ( the cell theory)

Pasteur (1859) - No living things arise by spontaneous generation. Microbes are everywhere - even in the air and dust The growth of microbes causes dead plant & animal tissue to

decompose & food to spoil (this led him to develop the technique of pasteurization - he developed it to keep wine from spoiling).

contributed to the development of vaccines.

 

III. ක්ෂුද්‍රජීවීන් වාර්ගීකරණය

ක්ෂුද්‍රජීවීන් පෑ�ධා�න කා�ණ්ඩා 5 ක් යටසෞත් වර්ග කාළ හා�කිය. එනම් බ�ක්ටීරිය�, ඇල්ගී, දිලී�, ප්‍

සෞ��ටසෞ��ව� �හා වෛව�ස් (bacteria, algae, fungi, protozoa, and viruses) සෞ1.  සෞමාමා කා�ණ්ඩා

අත� ද�කිය  හා�කි සෞපෑ�දු ලක්ෂණය පෑ�මා�ණසෞයන් ඉත� කුඩා� වීමායි.

වෛව�ස් වෛ�ලීය �Fවිධා�නයක් සෞන�දක්වයි.

අසෞනකුත් ක්ෂුද්‍රජීවීන් සෛසලීය ආක�ර 2 ක් යටගේත් හාදුනා� ගත හා�කිය. එනා�,

1. පෑ��3 නෂ්ටිකා (Prokaryotic -"before nucleus") – සෞමාමා වෛ�ල තුළ පෑටල වලින්

වටවූ වZහා (පෑටල වලින් වටවූ ඉන්ද්‍රකා� �හා නෂ්ටියක්) සෞන�මා�ත. ක්ෂුද්‍ර ජීවීන්

අතරින් බ�ක්ටීරිය�වන් පෑමාණක් පෑ��3 නෂ්ටිකා වෛ�ල �Fවිධා�නයක් ද�යි.

2. සුනෂ්ටිකා/ �ත නෂ්ටියක් �හිත (Eukaryotic -"true nucleus") – සෞමාමා වෛ�ල

තුළ පෑටල

වලින් වටවූ වහා (පෑටල වලින් වටවූ ඉන්ද්‍රකා� �හා නෂ්ටියක්) ඇත. ඇල්ගී, දිලී�, ප්‍

සෞ��ටසෞ��ව�, ශා�කා �හා �තුන් (protozoans, fungi, algae, animals, plants)  �ත න්

යෂ්ටිකා වෛ�ල �Fවිධා�නයක් ද�යි.

 

A.  බැ�ක්ටීරිය� (Bacteria)  

1. පෑ��3 නෂ්ටිකා සෞ1.

2. ඒකා වෛ�ලිකායි (unicellular) / ඝන�ව�� තනයි.  

වෛ�ල බිත්තියක් ඇත. වෛ�ල බිත්තිසෞ^ සෞපෑප්‍ටිසෞඩා�-3ලයිකා�න් අඩාFගු සෞ1.

වෛ�ල බිත්තියට පිටතින් කා�ප්‍සියුලය නම් සෞකා�පුවකින් ආව�ණය වී තිබිය හා�කා.

වලය�කා�� DNA අණුවක් තුළ වෛ�ල කිbය� පෑ�ලනයට අවශා පෑ�සෞ1ණිකා ද්‍රව

ගබඩා� කා� ඇත.

ප්‍ලස්මිඩා න�මාති කුඩා� වලය�කා�� DNA අණු ඇත. සෞම්ව� වෛජව ඉFජිසෞන්��

ත�ක්ෂණසෞ^ දී භ�විත� සෞ1.

පෑටල වලින් ආව�ණය වූ වෛ�ල ඉන්ද්‍රිකා� සෞන�මා�ත. සෞපෑ��ටීන �Fස්සෞල්ෂණයට

�යිබසෞ��මා ඇත.

3. පෑ�මා�ණය :  බ�ක්ටීරිය� වෛ�ලයක් දර්ශීය සුනෂ්ටිකා වෛ�ලයකින් 1/1000 ක් පෑමාණ

සෞ1.

4.  කා�ණ්ඩා 2 කි.

      a.  ආකිබ�ක්ටීරිය� Archaeobacteria : ආදි කා�ලීන බ�ක්ටීරිය�

      b.  ඉයුබ�ක්ටීරිය� Eubacteria - true bacteria : �ත බ�ක්ටීරිය�

5.     විවිධා හා�ඩා ඇත. බ�සිල� (bacillus-rod), සෞකා�කු� (coccus - spherical), �ර්පිල

(spirillum- spiral), සෞකා�මා� (vibrio -curved rod), ස්පෑයිසෞ��කීට (spyrochete –

long spiral)

6.     �චල සෞහා� අචල විය හා�කිය.

7.  ශාක්තිය ලබ� ගන්න� ආකා��ය අනුව විවිධාත්වයක් දක්වයි.

a. පෑ�භ�ස්වයFසෞපෑ�ෂකා (photosynthetic autotrophs) - සූර්යය ශාක්තිය භ�විත�

කා� අකා�බනිකා කා�බන් පෑ�භවය සෞල� CO2 සෞය�ද� ගනිමින් ශාකිති අවශාත�වය

�දහා� අවශා කා�බනිකා ආහා�� තමා� විසින්මා නිපෑදව� ගනියි(උද�:-

�යසෞන�බ�ක්ටීරිය�).

b. ���යනිකා ස්වයFසෞපෑ�ෂකා ( chemosynthetic autotrophs) - අකා�බනිකා

�Fසෞය�ග වලින් ශාක්තිය ලබ� සෞගන කා�බන් පෑ�භවය සෞල� CO2 සෞය�ද� ගනිමින්

කා�බනිකා ආහා�� තමා� විසින්මා නිපෑදව� ගනියි. (උද�:-දම් �ල්ෆර්/අයන්

බ�ක්ටීරිය�).

c. ���යනිකා විෂමා සෞපෑ�ෂකා (heterotrophs) - පිටතින් ලබ� ගන්න� කා�බනිකා

ආහා�� (උද�:-කා�සෞබ�හායිසෞlmට සෞහා� සීනි) වලින් තමා ශාක්ති අවශාත�වය �පු��

ගනියි.

d. පෑ�භ�විෂමා සෞපෑ�ෂකා (heterotrophs) - පිටතින් ලබ� ගන්න� කා�බනිකා ආහා��

වලින් තමා ශාක්ති අවශාත�වය �පු�� ගනියි.

8.     ස්ව�නය අනුව විවිධාත්වයක් දක්වයි.

a. ස්ව�යු- Acetobactor

b. වෛවකාල්පිත නිර්ව�යු - E.coli

c. අනිව�ර්යය නිර්ව�යු - Clostridium spp.

d. ක්ෂුද්‍ර ව�තකා�මී - Lactobacillus

9.    ජීවත්වන පෑරි��ය අනුව විවිධාත්වයක් දක්වයි. අධිකා උෂ්ණත්වයක් �හිත සෞමාන්මා

ඉත� පෑහාළ උෂ්ණත්වයක් �හිත පෑරි�� වල ද බ�ක්ටීරිය� ජීවත් සෞ1. ( -20oC to 110oC)

10. පෑ�ජනනය Cවී කාණ්ඩානය මාගින් සිදුසෞ1. වර්ධානය හා� පෑ�ජනනය ඉත� සෞ1ගසෞයන්

සිදුසෞ1.

11. ඇත�ම් බ�ක්ටීරිය�වන් ව�ධිජනකා සෞ1.

B.  ඇල්ගී  (Algae)

1.     සුනෂ්ටිකා සෞ1.

2.    ඒකා වෛ�ලිකා සෞහා� බහුවෛ�ලිකා සෞ1.   

3.    අන්වීක්ෂීය සෞමාන්මා අන්වීක්ෂීය සෞන�වන(උද�:- සෞකාල්පෑ) ඇල්ගී ��මා�ජිකායන් ද ඇත.  

4.      �චල සෞහා� අචල විය හා�කා.

5.      පෑ�භ��Fස්සෞල්ෂණය මාගින් ශාක්තිය ලබ� ග�නීමාට අවශා කා�බනිකා ආහා�� නිපෑදව� ගනී.

6.      ව�ධිජනකායන් සෞන�සෞ1.

 C. දිලීර   (Fungi)

1. සුනෂ්ටිකා සෞ1.

�Fවිධා�න�ත්මාකා වෛ�ල �Fවිධා�නයක් ද�යි. එනම් පෑටල වලින් ආව�ණය වූ න්

යෂ්ටිය, පෑටල වලින් ආව�ණය වූ වෛ�ල ඉන්ද්‍රිකා� , වෛ�ල පෑටල හා� වෛ�ල

ප්‍ල�ස්මායක් ඇත. හාරිතලව න�ත.

ඒකා නෂ්ටිකා/බහු නෂ්ටිකාසෞ 1.

වෛ�ල බිත්තියක් ඇත. වෛ�ල බිත්තිසෞ^ කායිටීන් අඩාFගු සෞ1. කායිටීන්

සෞtපෑ�ලි��කා�යිඩායකි.

සෞපෑ��ටීන �Fස්සෞල්ෂණයට �යිබසෞ��මා ඇත.

2. ඒකා වෛ�ලිකා සෞහා� බහුවෛ�ලිකා සෞ1. උද�:-

ඒකා වෛ�ලිකා -යීස්ට්

බහු වෛ�ලිකා - සූතිwකා�කා�� දිලී� ; එමා සූතිwකා� ��ව�� සෞහා� නි��ව�� විය හා�කා.

සූතිwකා� සියල්ල එක්ව ගත් විට මායිසීලියමා සෞල� හා�දින්සෞ1.   

3.    අචල සෞ1. / අt�ත�ම් -�චල -

4 විෂමාසෞපෑ�ෂී සෞ1. මාIසෞත�පෑජීවීන් සෞල� මිය ගිය ශා�කා හා� �ත්ත්ව සෞකා�ටස් විසෞය�ජනය

කා� සෞපෑ�ෂණය ලබ� ගනී. පෑ�භ��Fස්සෞල්ෂණය සෞන�කා�යි.

5. �Fචිත ආහා��ය 3ලයිසෞකා�ජන් සෞ1.

6.    ඇත�ම් දිලී� පෑ�සෞපෑ�ෂිතයන් වන අත� තවක් �මාහා�ක් අසෞන�න�ධා��කායන්සෞ1.

(උද� : දිලී�කාමූල)

7. ව�ධිජනකා සෞන�වන දිලී� වර්ග ද ව�ධිජනකා වන දිලී� වර්ග ද සෞ1.

8. ලිFගිකා පෑ�ජනනය / අලිFගිකා පෑ�ජනන දක්වයි.

අලිFගිකා - මායිසීලියමාසෞ කා�ටස් වලට කා�ඩීය�මා/ අFකු�ණය/ අලිFගිකා බීජ�නු

ලිFගිකා පෑ�ජනනය - බීජ�නු මාගින් සිදු කා�යි.

  D.  ගේ78�ගේට�ගේස9වා�   (Protozoa - "first animals")

1.   සුනෂ්ටිකා සෞ1.

2.   ඒකා වෛ�ලිකා සෞහා� බහුවෛ�ලිකා සෞ1.   

3.   අන්වීක්ෂීය සෞමාන්මා අන්වීක්ෂීය සෞන�වන(උද�:- සෞකාල්පෑ) ඇල්ගී ��මා�ජිකායන් ද ඇත.  

4.   �චල සෞහා� අචල විය හා�කා.   

5. විෂමාසෞපෑ�ෂී සෞ1. මාIසෞත�පෑජීවීන් සෞල� මිය ගිය ශා�කා හා� �ත්ත්ව සෞකා�ටස් මාත

ය�සෞපෑමින් මාගින් ශාක්තිය ලබ� ග�නීමාට අවශා කා�බනිකා ආහා�� ලබ� ගනී.

6.  ඇත�ම් ��මා�ජිකායන් ව�ධිජනකා සෞ1. (උද�: මා�සෞල්රිය� , ඇමීබ� අතී���ය)

 

E.  සෛවාරස් (viruses)

1.   වෛ�ලීය �Fවිධා�නයක් සෞන�දක්වයි. එමා නි�� පෑ��3 නෂ්ටිකා සෞහා� සුනෂ්ටිකා සෞල�

ද�ක්විය සෞන�හා�කා.

2. අනිව�ර්ය අන්තර් වෛ�ලීය පෑ�සෞපෑ�ෂිතයන් සෞ1. ධා��කා වෛ�ලසෞයන් පිටත දී �ජීවී ව

පෑ�වතිය හා�කි බවට ��ධාකා න�ත.

3.   වෛව��යකා මූලිකා වZහාය: කා�ප්‍සිඩාය නම් වූ සෞපෑ��ටීන සෞකා�පුවකින් වට වූ නෂ්ටිකා

අම්ල (RNA or DNA) අණුවක් ද�යි ; නෂ්ටිය, වෛ�ල ඉන්ද්‍රකා� , වෛ�ල පෑටල සෞහා�

වෛ�ල ප්‍ල�ස්මායක් සෞන�මා�ත.

4.   පෑ�මා�ණය: බ�ක්ටීරිය� වෛ�ලයකින් 1/10 to 1/1000 ක් දක්ව� පෑ���යකා ^20 nm-

300 nm)

5.   ව�ධිජනකාය : සෞවනත් ජීවීන් ආ��දනය කිරීසෞම් හා�කිය�ව ඇත.

6. හා�ඩාය අනුව මූලිකා ආකා�� 2 කි. එනම් Polyhedral �හා Helical සෞ1.

7.   චලනය විය සෞන�හා�කා.

 III.       A Brief History of Microbiology 

C.        Leeuwenhoeck (lived 1632-1723)1.       What discovery is he credited with?  First person to use microscopes

to observe microbes; as a hobby he made small handheld microscopes; he called microorganisms “animalcules.”

 C.       Hooke

1.       What discovery is he credited with?  He first described “cellulae” (small rooms) in cork in 1665.  His discovery led to the formulation of the cell theory, which states that cells are the basic organizational unit of all living things.

 C.       Redi and Spontaneous Generation

1.       What is this theory? Living organisms arise from nonliving things (ex. maggots come from rotting meat)

2.     Who disproved this theory and how?  In the late 1600’s Francisco Redi showed that maggots developed only in meat that flies could reach to lay eggs on. 

3.     Many insisted that he only disproved spontaneous generation for macroorganisms; maybe microbes were an exception.

 D.      Needham vs. Spallanzani - still trying to prove or disprove the theory of spontaneous

generation.1.       What was Needham's hypothesis, experiment, &

conclusions?  Everyone knew boiling killed microbes; so, he would boil chicken broth, put it in a flask, & seal it; if microbes grew, then it could only be because of spontaneous generation; they did grow.  [We now know that microbes grew because the flask was not sterilized before he poured in the broth!]

2.     What was Spallanzani's hypothesis, experiment, & conclusions?  He was not convinced by Needham's experiment.  He put broth in a flask, sealed it (creating a vacuum), & then boiled it.  There were no microbes in the cooled broth!  Critics said he didn't disprove spontaneous generation - they said he just proved that spontaneous generation required air.

           E.  Pasteur's Epic Experiments (1859)

1.       What was his experimental method?  To offset the argument that air was necessary for spontaneous generation, Pasteur allowed the free passage of air, but prevented the entry of microbes.  He boiled meat broth in a flask & then drew out & curved the neck of the flask in a flame.  No microbes developed in the flask. When he tilted the flask so some broth flowed into the curved neck & then tilted it back so the broth was returned to the base of the flask, microbes grew. Gravity had caused the microbes that had entered the flask in air & dust to settle at the low point of the neck, never reaching the broth in the base until the broth washed them in.  

 2.     Pasteur's success was partly due to good luck.  He used meat, which

contains few bacterial endospores (endospores are resistant to heat; many experiments done prior to Pasteur's used vegetable broths - plants contains many endospore-forming bacteria.)

                    3.  What 3 things did Pasteur's experiments prove? 

a.        No living things arise by spontaneous generation.b.       Microbes are everywhere - even in the air and dust

c.        The growth of microbes causes dead plant & animal tissue to decompose & food to spoil (this led him to develop the technique of pasteurization - he developed it to keep wine from spoiling).

 4.  Pasteur also contributed to the development of vaccines.

           F.  The Germ Theory of Disease

1.       What is the germ theory of disease?  Microbes (germs) cause disease and specific microbes cause specific diseases.

2.     Who proved this theory?  Robert Koch in the late 1870's.3.     What disease was he studying?  anthrax - disease of cattle/sheep;

also in humans4.     What was his experimental method?  He observed that the same

microbes were present in all blood samples of infected animals.  He isolated and cultivated these microbes (now known to be Bacillus anthracis ).  He then injected a healthy animal with the cultured bacteria & that animal became infected with anthrax & its blood sample showed the same microbes as the originally infected animals. 

5.     What did his experiments prove?  Particular microbes cause particular diseases.

                   6.   What are Koch's 4 Postulates?1.)     The causative agent must be present in every individual

with the disease.2.)   The causative agent must be isolated & grown in pure

culture (how did he invent pure cultures?; with Frau Hesse's help, he developed the agar plate method (see p. 13).

3.)   The pure culture must cause the disease when inoculated into an experimental animal.

4.)   The causative agent must be reisolated from the experimental animal & reidentified in pure culture.

           G.  What are Some Ways that We Can Control Infectious Diseases? 

1.       Immunity - stimulating the body's own ability to combat infection; from ancient times it was a recognized fact that people who suffered from certain diseases never got them again; infection could produce immunity.

a.      Immunization defined:  produce immunity by providing exposure to altered organisms that do not cause disease.

b.     Jenner & Smallpox - observed that dairymaids that contracted a mild infection of cowpox seemed to be immune to smallpox.  He inoculated a boy with fluid from a cow pox blister and he contracted cowpox; he then inoculated him with fluid from a smallpox blister; the boy did not contract smallpox; the term vaccination came from vacca  for cow. 

                             c.  The first vaccines:1.)    Pasteur's discovery? attenuated bacteria can

produce immunity2.)   Attenuated defined - weakened virus or bacteria that

is unable to cause the disease (it was later discovered that killed microbes can also produce immunity)

3.)   What vaccines did Pasteur develop?  anthrax, rabies                    2.  Public Hygiene

                             a.  Improving sewage disposal.                             b.  Assuring a clean public water supply.                             c.  Food preservation & inspection.                                      ex. Pasteurization - kills most microbes by exposing to heat.                             d.  Improving personal hygiene.                                      Semmelweiss & childbed fever               

e.  Developing antiseptic techniques.Lister & carbolic acid  – he developed the first aseptic techniques.

  3.  Chemotherapy     a.      Who is the father of chemotherapy?  Paul Ehrlich - he discovered a drug treatment for syphilis; he developed the guiding principle of chemotherapy, which is selective toxicity  (the drug must be toxic to the infecting microbe, but relatively harmless to the host’s cells).  b.     What was the first major class of drugs to come into widespread clinical use?  sulfa drugsc.      Who discovered the first antibiotic?  Flemming discovered (penicillin); antibiotics are antibacterial compounds produced by fungi and bacteria.        

CHAPTER 2 – INTRODUCTORY CHEMISTRY & BIOCHEMISTRY

 

INTRODUCTORY CHEMISTRY

Why is it necessary to study chemistry?  Living things are made of matter (anything that occupies space & has mass) & matter follows the laws of chemistry.  Even the characteristics we consider to be unique to living things are the result of chemical reactions (ex. movement as a result of muscle contractions).

 

I.  THE ATOM

A.    Atom - smallest unit of matter unique to a particular element.

B.     Element - A substance made up of only one kind of atom - ex. carbon contains only carbon atoms.  Elements can't be broken down into other substances by ordinary chemical means.  Each element displays unique properties (ex. some are gases, some are solids, some are metals, etc.). About 92 elements occur naturally (there are also some man-made elements).  Some of the elements important to our study of living systems are carbon, oxygen, hydrogen, nitrogen, sodium, chlorine, phosphorus, and potassium.  You may also be familiar with the elements lead, iron, iodine, gold, silver, and copper, nickel, and platinum.

       C.  Some Important Things to Know about Atoms & Elements:

              1.  An atom consists of 2 basic parts: 

                             a.  nucleus - the nucleus contains protons & neutrons:

1.) protons - positively charged; all atoms have protons; protons give the nucleus a positive charge.                               

2.) neutrons - neutral in charge; fxn.: "stabilizers"; all atoms except hydrogen have one or more neutrons.

b.    electrons – negatively charged; occupy orbit energy levels or shells around the nucleus; attracted to the positive charge of the nucleus; in an atom, the number of electrons always equals the number of protons, so the atom, as a whole, has no charge; electrons determine the chemical properties of elements (ex. whether they are a liquid, solid, or gas, etc.).

2.    atomic number = number of protons (or number of electrons); in an atom, the number of protons always equals the number of electrons; this number differs for each element.

3.    atomic mass number = number of protons + number of neutrons; the number of electrons is not included in the mass number due to their insignificant mass.

4.    The 6 elements important for building organic molecules like carbohydrates, lipids, proteins, and nucleotides are: carbon, hydrogen, oxygen, sulfur, nitrogen, & phosphorus.

 Note:  Be able to determine the number of electrons, protons, & neutrons in an atom, given the atomic number & atomic mass.  Ex. Sodium (Na) has an atomic number of 11 & an atomic mass of 23.  A Sodium atom has 11 protons, 11 electrons, & 12 neutrons.

 

II.            CHEMICAL REACTIONS

 

A.  More about Electrons

1.    Electrons orbit around the nucleus at different energy levels or shells the 1st shell (k shell) can hold no more than 2 electrons; the next shell (l shell) can hold 8 electrons, 2 electrons in each of 4 orbitals; the next shell (m shell) also holds 8 electrons. These will be the only shells that we will deal with in this class.

2.    An atom is the most stable when all of its shells are completely filled (the k shell fills first, then the l shell, then the m shell, & so on).

3.    The atoms of many elements have partially filled outer shells, therefore they are not very stable; these atoms tend to react with other atoms to completely fill their outer shells &, in doing so, they form chemical bonds; it is important to remember that it's the electrons of an atom that participate in the chemical bonds that form between atoms.  Molecules are formed when 2 or more atoms are joined together by interactions between the electrons of their outer electron shells.

 

B. Chemical Bonds

       1.  Ionic bonds

a.    definition - in ionic bonds electrons are transferred to other atoms to completely fill outer shells; atoms are electrically neutral, but when they gain or lose electrons in combining with other atoms, they are called ions (charged atoms) & they take on a positive or negative charge; in other words, the transfer of electrons upsets the balance of protons & electrons in an atom; atoms that lose electrons are positively charged, atoms that gain electrons are negatively charged; ionic bonds involve the attractions between these oppositely charged ions.  So, before you can have an ionic bond, you have got to have oppositely charged ions, & to create ions you have got to transfer electrons.       

b.    example:  NaCl (sodium chloride- table salt); Na (at. # 11) has one electron in its outer m shell - it needs 7 electrons to fill this shell - it is easier for Na just to give this electron away, & eliminate the m shell entirely.  Cl (at. # 17) has 7 electrons in its outer m shell - it only needs 1 electron to fill its outer shell. Therefore, when Na & Cl atoms react, Na gives up its outer electron to Cl.  Because Na gives up an electron, it now has 11 protons & 10 electrons, resulting in a positively charged atom.  Cl now has 17 protons & 18 electrons, resulting in a negatively charged atom.  Na+ & Cl- ions are attracted to each other because of

their opposite charges & an ionic bond is formed.  The attraction is the ionic bond!  Only the electron # changes when ions are formed!

 

       2.  Covalent bonds - more common in the human body & are more stable.

a.    definition - Electrons are not transferred, but are shared.  The shared electrons spend part of their time around the nucleus of one atom & part of their time around the other.  Each pair of electrons shared equals one covalent bond (if 2 pair of electrons are shared between 2 atoms, a double covalent bond is formed, a triple covalent bond occurs when 3 pr. of electrons are shared).  We only discuss single covalent bonds.

b.    example:  methane (CH4);  a carbon atom can form four covalent bonds - it has 4 electrons in its outer shell, therefore it needs 4 more electrons to fill its outer shell; hydrogen has one electron in its outer shell, therefore it needs one electron to fill its outer shell.  Rather than give 4 electrons away or accept 4 electrons, carbon shares its 4 electrons in its outer shell with 4 Hydrogen atoms. 

c.     polar vs. nonpolar - covalent bonds can be polar or nonpolar; if both atoms exert the same pull on the shared electrons (equal sharing), the bond is nonpolar (example: methane); if there is unequal sharing of electrons, the bond is polar; in molecules with polar covalent bonds, there is an atom that has a much larger nucleus (more protons) than the other atoms in the molecule; the atom with the most protons is more attractive to the shared electrons, so the electrons spendmost of their time around this atom's nucleus; all of these electrons spending most of their time around a particular nucleus gives this part of the molecule apartial negative charge; the other atom(s) in the molecule acquire a partial positive charge, because the shared electrons are not spending much time around them.  Shared electrons in polar covalent bonds are not spending all of their time around a particular nucleus - if this were the case then we would be talking about electrons being transferred (as in ionic bonds).

4.    Hydrogen bonds - These bonds result from polar covalent bonds; they form between   molecules  & occur between the slightly negative atom of one molecule & the slightly positive atom of another molecule.  These bonds can occur between hydrogen & oxygen & between hydrogen & nitrogen.  Hydrogen bonds are weaker than ionic & covalent bonds, because the charges on the molecules are "partial" or weak charges.

 

C.     Chemical Reactions - A chemical reaction when atoms or molecules (called reactants) collide and are transformed into different combinations of the same atoms or molecules (called products).  In this process, chemical bonds break and new ones form.  In living systems special proteins called enzymes catalyze these chemical reactions (they make them “go”).  We'll talk more about enzymes later.

 III.  WATER

 A.  Structure:

 

1.    A single water molecule is made up of one oxygen atom & two hydrogen atoms (H2O).

 

2.    Oxygen has 8 protons, while each hydrogen has only one proton.  Oxygen forms a covalent bond with each hydrogen so that the outer shells of each atom are complete.

 

3.    Because the oxygen atom has more protons (positives) than the hydrogen nuclei, the shared electrons have a greater attraction to the oxygen nucleus & spend more time around it than they do around the hydrogen nuclei (unequal sharing of electrons).  The oxygen atom therefore has 10 electrons (8 of its own & 1 from each hydrogen) spending most of their time around its nucleus of 8 protons - this gives the oxygen end of the water molecule a partially negative charge.  Since the hydrogen electrons are spending most of their time around the oxygen atom, the hydrogen atoms, which have one proton each, take on a partially positive charge.  This results in apolar molecule (a molecule that has partially positive & negative regions).  Their polarity allows water molecules to interact with one another, forming hydrogen bonds. The same type of interaction is possible between water & many other polar substances.  Polar substances are hydrophilic (water-loving) & nonpolar substances arehydrophobic (water-fearing). 

 

B.    PROPERTIES OF WATER - Hydrophilic & hydrophobic interactions underlie several properties of water that are biologically important.

 

       1.  Temperature-Stabilizing Effects:

 

Note:  The temperature of a substance is a measure of how fast its molecules are moving; the higher the temperature of a substance, the faster its molecules are moving.

 

a.) heating water - It takes considerable heat to raise the temperature of water because the hydrogen bonds between the water molecules restrict the movement of the molecules; in order for the temperature of water to rise, a number of H bonds must be broken - this takes a lot of energy.  This resistance to temperature change helps living cells to maintain a relatively constant temperature; this is important because biochemical reactions take place within a narrow temperature range (this has to do with the action of enzymes).  This resistance to temperature change also helps organisms that live in aquatic or marine environments.

 

2.    Water As a Solvent - the polarity of water is also responsible for water's capacity as a solvent (something that dissolves something else); water is an excellent solvent for ions & other polar molecules (solutes) in cells.

 

 

C.  ACIDS AND BASES

When molecules of inorganic acids, bases, or salts dissolve in water of body cells, they undergo ionization or dissociation (they break apart into their individual ions).

 

1.       Acids & Bases Generally Defined

 

Acid - Defined as a solute that releases H+ ions in a solution 

[ex. HCl - hydrochloric acid dissociates into H+ ions & Cl- ions]

 

Base - Defined as a solute that removes H+ ions from a solution; many release OH- ions in this process.

[ex. Mg(OH)2  - magnesium hydroxide dissociates into OH- ions & Mg++ ions].

 

2.    pH Scale - Fluids are assigned a pH value (0 -14), which refers to the hydrogen ion concentration present in the fluid.  The hydrogen ion concentration is abbreviated as [H+].

 

a.     acid - pH below 7.0; base - pH above 7.0; neutral - pH = 7.0

b.     pH = - log [ H+ ]  (formula for calculating pH)

c.     It is a common misconception to think that as the [H+] increases, the pH also increases!  The rule is:  As [H+] increases, pH decreases!  This can be seen from the following example:

                             solution A:   [H +] = 1 x 10-2  or 0.01              pH = -log[1 x 10-3] = 2

                             solution B:   [H+ ] = 1 x 10-8 or 0.00000001   pH = -log[1 x 10-4] = 8

 

(A quick way to find the pH of these solutions is to look at the exponent or count the number of decimal places in the [H+])

 

Solution A is more acidic than Solution B - Solution has a higher [H+] than Solution B (0.001 > 0.0001); therefore, Solution A has a lower pH than B.

 

When you think about a pH value, think that this number is really the number of decimal places in the hydrogen ion concentration.  The larger the number, the more decimal places there are, indicating a smaller hydrogen ion concentration.

 

3.    Buffers - help maintain a constant pH by removing or adding H+ ions; the pH inside living systems is generally between 7.35-7.45 (exception: the hydrochloric acid in the digestive system makes the pH here 2-3); this pH range is important, as many biochemical reactions take place only within this range; buffers can combine with hydrogen ions &/or release them, & so help stabilize the pH.

 

BIOCHEMISTRY 

4 Groups of Organic Compounds Important in Living Organisms:

Carbohydrates        Lipids       Proteins         Nucleotides

 

Organic compound defined – A compound containing carbon (with exception of carbon dioxide); found in all living things.

 

THE CENTRAL ROLE OF CARBON

 

A.   The Carbon Backbone - The processes of life are primarily the result of the chemistry compounds of carbon.  Because of carbon's tendency to form four covalent bonds in four different directions, carbon can form an unbelievably large number of different compounds of high complexity; organic compounds derive their basic shapes from the carbon atoms; this shape helps determine the compound's function in living systems.

 

B.    Functional groups - The structure & behavior of organic compounds also depends on the properties of their functional groups; functional groups are groups of atoms (ex. hydrogen, oxygen, nitrogen, phosphorus, sulfur) attached to the carbon backbone. 

 

 

I.     CARBOHYDRATES:

 

A.  Structure:  generally made up of only three elements:  carbon, hydrogen, & oxygen

      

B.  Three Principle Classes of Carbohydrates:

       1.  Monosaccharide

a.    Structure - composed of single sugar molecule; the atoms in a sugar molecule can form a straight chain or a ring (rings are more common in the body).

b.    Examples - Glucose, Ribose, Fructose, Galactose

d.    Functions - monosaccharides are important energy molecules in living things; glucose is the primary energy source for humans & many other animals; also important as building blocks of larger sugars.

 

      

    

2.  Oligosaccharides - composed of short chains of monosaccharides;  Examples:  

a.    Sucrose (table sugar) is a disaccharide composed of glucose & fructose; sucrose is the form in which sugars are transported in plants.

b.    Lactose (milk sugar) is a disaccharide composed of glucose & galactose.

 

 

 

   

 

                              Sucrose =   Glucose       +         Fructose

 

2.         Polysaccharides - straight or branched chains of many monosaccharide units

 

              a.  Storage Polysaccharides

1.)  Starch - sugar storage in plants.

2.)  Glycogen – “animal starch;” principle storage form for glucose in higher animals; this energy storage is short term; lipids are used for long term energy storage.

 

                   b.  Structural Polysaccharides

1.) Cellulose – Principal component of the plant cell wall; also found in the cell walls of algae and fungi.  Monosaccharides are bonded together in such a way that the molecule resists breakdown by multicellular organisms.  We don’t have the digestive enzymes to break the bonds; however, some microorganisms do have these enzymes; this is why microbes are so important in the gut of a termite, cow, etc.)

2.) Chitin – contains nitrogen; forms the cell wall of some fungi (it’s the same stuff insect exoskeleton’s are made of!)

II.     PROTEINS

 

A.   Protein Structure:

 

1.    Proteins are composed of subunits called amino acids (there are 20 different amino acids that make up proteins).  Amino acids contain carbon, hydrogen, oxygen, and nitrogen.  Some also contain sulfur.  Amino acids have a structure similar to the one below.   The R stands for some other atom or group of atoms bonded to the central carbon atom in the molecule.  The sequence of amino acids in a chain helps determine the structure & shape of the protein & therefore the function of the protein; there are many possible combinations of amino acids that produce the many different kinds of proteins.                                                                      

 

   H           H            O

 

N----C----C

 

   H          R           OH     

 

2.    Peptide bonds - linkage formed between one amino acid & another amino acid; the name of these bonds is why chains of amino acids are called polypeptides.

 

3.    Producing the three dimensional structure of a protein:  We have been discussing proteins as "chains of amino acids."  However, the final structure of proteins is not a straight chain of amino acids.  Proteins are very complex, three-dimensional molecules, with numerous twists & folds.  The amino acid chain of every kind of protein is folded in a very specific way [the chain will twist & fold itself based on the linkage of amino acids in a specific sequence & the environmental conditions (i.e., temperature & pH)].  There are several bonds & forces which give a protein its specific 3-D structure (i.e., hydrogen bonds, ionic bonds, etc.); these bonds link distant parts of the molecule, forming loops, twists, etc.  Destruction of a protein's 3-D structure by extreme heat or pH is called denaturation (see "enzymes" on the next page for how this occurs).  Analogy for protein structure: Think of a phone cord.  Pull it straight (like a straight chain of a.a.), then let it twist, then roll the twisted cord into a ball.  (Every type of protein folds and twists in a very specific way.)      

B.      Some Specific Functions of Proteins:

1.    Structural Proteins: collagen in connective tissue, keratin in the skin, cytoskeleton in cells

2.    Functional Proteins:

a.    membrane transport proteins – transport substances across the cell membrane

b.    cell movement – ex. flagellum

c.     enzymes as catalysts (enzymes speed up the rate of chemical reactions); all life processes are primarily the result of chemical reactions; molecules in living things require enzymes in order to react; without enzymes, chemical reactions in living things can’t occur; see below for more information on enzymes.

d.    antibodies in the immune response

 

C.    Enzymes – a large, globular protein molecule that accelerates a specific chemical reaction.  Virtually all chemical reactions that take place in cells involve enzymes!!!  Most of a cell’s proteins are enzymes.

 

1.       Why are enzymes needed?  In order for particular molecules to react with one another, they must be in close proximity & must collide with sufficient force to overcome the mutual repulsion of their negatively charged electron clouds & to break existing chemical bonds within the molecules.  The force with which they collide depends on their kinetic energy (energy of motion).  Most chemical reactions require an initial input of energy to get started, which increases the kinetic energy of the molecules, enabling a greater number of them to collide with sufficient force.  In the chemistry lab, we can supply this energy with heat.  In a cell, many different

reactions are going on at the same time, therefore heat cannot be used as it would be nondiscriminatory (it would affect many reactions at the same time).  Cells get around this problem by using enzymes, which serve as catalysts (they get the chemical reactions going).  The enzymes form a temporary association with the molecules that are to react, bringing them close to one another & weakening the existing chemical bonds, making it easier for new ones to form.           

 

2.    Enzyme Structure & Function - Enzymes are large, complex, globular proteins consisting of one or more polypeptide chains.  The molecules that enzymes acts on are known as the substrates.  Enzymes are folded to form a groove or pocket (called an active site) on their surface into which the substrate fits & where the chemical reactions take place.  See diagram below:

 

3.    Effects of Temperature & pH on Enzyme Function 

1.    Temperature:  As the temperature increases, so does the rate of enzyme catalyzed reactions, but only up to a certain point.  At high temperatures, the enzymes are denatured (due to the vibration of molecules at high temperatures, the bonds that maintain the enzyme's structure are broken & the protein unfolds). If denaturation is severe, the damage to the enzyme is irreversible.  

2.    pH:  The shape of the enzyme depends partly on attraction between positively & negatively charged amino acids.  As the pH changes (acidic - more H+, basic - fewer H+), these charges change, changing the shape of the enzyme & its function.  Remember:  the optimum pH for most enzymes is 6-8. (exception:  the stomach which has a pH of 2)

 

Note:  All proteins can be denatured by heat and extreme pH.

  

III.  PEPTIDOGLYCANThis molecule has both protein and polysaccharide components and it forms the cell wall of eubacteria.  It may be one or several layers thick.  It is an extremely strong protective covering.  Glycan strands in all eubacteria are made of alternating units of 2 modified sugars, N-acetylglucosamine (NAGA) and N-acetylmuramic acid (NAMA). (It’s structure is similar to a chain link fence!)  More later!

  

IV.  LIPIDS

A.     General Structure - all lipids are mostly nonpolar (hydrophobic) & are insoluble in polar solvents such as water; lipid structure varies greatly & is discussed below for each type.

B.      Some General Functions:                       

1.    long term energy storage (example:  glycerides); energy is stored in the chemical bonds; excess carbohydrates, proteins or fats are converted to triglycerides & are stored in adipose (fat) tissue.

          2. structural (example:  phospholipids make up the cell membrane of cells)

C.  Types of Lipids:

 

       1.  Lipids with Fatty Acids – Glycerides & Phospholipids:

a.    Glycerides

1.)             Structure:   classified as mono-, di-, & triglycerides, depending on the number of fatty acids attached a single glycerol molecule; glycerol has 3 carbon atoms & 3 hydroxyl (OH) groups; fatty acids are long, nonpolar chains composed of hydrogen & 4 to 24 carbon atoms, with a carboxyl (COOH) group at one end.

 

a.)  Saturated fatty acids - all carbons in the fatty acid tails are joined together by single carbon to carbon bonds & as many hydrogen atoms as possible are linked to the carbons (the carbons are said to be "saturated" with hydrogens); triglycerides with many saturated fatty acids are solid at room temperature; occur mostly in animal tissues, but also in a few plant products; examples: butter, lard, cocoa butter, palm oil, coconut oil; the liver produces cholesterol from some breakdown products of saturated fats.

b.) Unsaturated fatty acids - one or more double bonds occur between carbon atoms in the fatty acid tails; this cuts down on the number of hydrogen atoms that can bond to the carbons; liquids at room temperature; the double bonds create a kink in the shape of the molecule prevent the fatty acids from packing close together & becoming solidified; unsaturated fatty acids are more common in plants; monounsaturated fatty acids are better for you that the polyunsaturated ones; the poly’s can produce compounds called trans fatty acids, which increase the risk of heart disease.

A triglyceride molecule:

              H                   H    H   H    H   H    H    H   H    H   H      

            H--C---O---C--C—C--C--C--C—C—C—C—C--C—H       saturated f.a.

                             O   H   H    H   H   H    H    H   H    H   H  

 

                                    H    H   H   H   H    H    H   H    H   H             

            H--C---O---C--C—C--C--C--C--C—C—C—C—C--H      saturated f.a.

                                 O   H    H   H    H   H   H    H   H    H    H  

 

                                       H    H   H    H    H   H    H   H    H    H                     

            H—C---O---C—C—C—C==C—C—C—C—C—C—C---H    unsaturated f.a.

                 H             O    H    H                H   H    H   H    H   H  

         

                     2.)  Functions of Glycerides

a.) Energy - For most organisms and cellular microorganisms, sugars in excess of what can be stored as glycogen are converted into fats for more permanent storage; this is not the case in bacteria!

                          

              b.  Phospholipids

1.) Structure - 2 fatty acids & 1 phosphate group are linked to a glycerol molecule; a small polar group is linked to the phosphate group; this results in a molecule with a dual nature - the molecule has a nonpolar, hydrophobic end & a polar, hydrophilic end.

 

2.) Function:  Structural.  The phosphate end of the molecule & its polar group are called the "head" of the molecule; the two fatty acids are called the "tails" of the molecule; the head is hydrophilic ("water-loving"), while the 2 fatty acid "tails" are hydrophobic ("water-fearing").  This arrangement forms the structural basis ofcellular membranes & is called the phospholipid bilayer.

 

   Phosphate Head (polar)

2 Fatty AcidTails (nonpolar)

          V                                 

       2.  Lipids without Fatty Acids:  Steroids

a.    Structure - different from other lipids; they consist of 4 interlocking carbon rings with numerous hydrogens attached; while they have no fatty acids, they are still nonpolar & hydrophobic, so they are classified as lipids.

   

 

     

                   b.  Some Examples:

1.) cholesterol - important component in eukaryotic cell membranes & serves as the starting material for the synthesis of other steroids.  Not found in the cell membranes of bacteria with the exception of the Mycoplasms.

V.     NUCLEOTIDES

             

A.  Structure:   nucleotide = phosphate(s) + monosaccharide + a nitrogen-containing compound (called a base); it’s the bases that spell out the genetic message in DNA & RNA).

 

B.  Functions:

 

       1.    Nucleotides are the basic subunits of nucleic acids such as

 

a.    DNA (deoxyribonucleic nucleic acid) - carrier of the genetic message - makes up chromosomes in the nucleus of the cell.

 

b.    RNA (ribonucleic acid) - transcribes genetic message present in DNA & produces proteins from it. 

 

2.    Nucleotides also make up the adenosine phosphates (ex. ATP - adenosine triphosphate – used for energy molecule in the cell).

 

3.    Nucleotides make up some coenzymes (ex. NAD & FAD); these molecules function as electron carriers in some biochemical reactions; they are called the cell’s “reducing power.”  We’ll talk about this more in the metabolism chapter.